CellWhere: graphical display of interaction networks organized on subcellular localizations.

Lu Zhu, Apostolos Malatras, Matthew Thorley, Idonnya Aghoghogbe, Arvind Mer, Stephanie Duguez, Gillian Butler-Browne, Thomas Voit, William Duddy

    Research output: Contribution to journalArticle

    Abstract

    Given a query list of genes or proteins, CellWhere produces an interactive graphical display that mimics the structure of a cell, showing the local interaction network organized into subcellular locations. This user-friendly tool helps in the formulation of mechanistic hypotheses by enabling the experimental biologist to explore simultaneously two elements of functional context: (i) protein subcellular localization and (ii) protein-protein interactions or gene functional associations. Subcellular localization terms are obtained from public sources (the Gene Ontology and UniProt-together containing several thousand such terms) then mapped onto a smaller number of CellWhere localizations. These localizations include all major cell compartments, but the user may modify the mapping as desired. Protein-protein interaction listings, and their associated evidence strength scores, are obtained from the Mentha interactome server, or power-users may upload a pre-made network produced using some other interactomics tool. The Cytoscape.js JavaScript library is used in producing the graphical display. Importantly, for a protein that has been observed at multiple subcellular locations, users may prioritize the visual display of locations that are of special relevance to their research domain. CellWhere is at http://cellwhere-myology.rhcloud.com.
    Original languageEnglish
    Pages (from-to)W571-W575
    JournalNucleic Acids Research
    Volume43
    Issue numberW1
    Early online date16 Apr 2015
    DOIs
    Publication statusE-pub ahead of print - 16 Apr 2015

    Keywords

    • Muscle
    • Subcellular localization
    • graphical display
    • protein-protein interction

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    Cite this

    Zhu, L., Malatras, A., Thorley, M., Aghoghogbe, I., Mer, A., Duguez, S., Butler-Browne, G., Voit, T., & Duddy, W. (2015). CellWhere: graphical display of interaction networks organized on subcellular localizations. Nucleic Acids Research, 43(W1), W571-W575. https://doi.org/10.1093/nar/gkv354